Adolescent Social Structure by by Jim Moody

Adolescent Social Structure by by Jim Moody

The political blogosphere and the 2004 election: Divided they blog by Lada Adamic

Network Map of Protein-Protein Interactions by Erich E. Wanker of the Max Delbrück Center for Molecular Medicine (MDC)

BIT Formation

International Conflict Event Warning System (ICEWS): Material Conflict by Minhas, Hoff, & Ward

• What makes network data particular?
• Social Relations Model
• Latent variable models
• Additive and Multiplicative Effect Networks (amen)
• Does it work? Real world application
• Does it work? Simulation exercise
• What's next?

Relational data consists of

• a set of units or nodes
• a set of measurements, \(y_{ij}\), specific to pairs of nodes (i,j)

GLM: \(y_{ij} \sim \beta^{T} X_{ij} + e_{ij}\)

Networks typically show evidence against independence of {\(e_{ij} : i \neq j\)}

Not accounting for dependence can lead to:

• biased effects estimation
• uncalibrated confidence intervals
• poor predictive performance
• inaccurate description of network phenomena

We've been hearing this concern for decades now:

# library(devtools) ; devtools::install_github('s7minhas/amen')
library(amen) # Load additive and multiplicative effects pkg
data(IR90s) # Load trade data

Y[1:5,1:5] # Data organized in an adjacency matrix

##           ARG        AUL       BEL        BNG        BRA
## ARG        NA 0.05826891 0.2468601 0.03922071 1.76473080
## AUL 0.0861777         NA 0.3784364 0.10436002 0.21511138
## BEL 0.2700271 0.35065687        NA 0.01980263 0.39877612
## BNG 0.0000000 0.01980263 0.1222176         NA 0.01980263
## BRA 1.6937791 0.23901690 0.6205765 0.03922071         NA

# Reciprocity
cor(c(Y), c(t(Y)), use='complete')

## [1] 0.9392867

# Reciprocity beyond nodal variation?
senMean = apply(Y, 1, mean, na.rm=TRUE)
recMean = apply(Y, 2, mean, na.rm=TRUE)
globMean = mean(Y, na.rm=TRUE)
resid <- Y - ( globMean + outer(senMean,recMean,"+"))
cor(c(resid), c(t(resid)), use='complete')

## [1] 0.8591242

• The patterns mentioned above can be represented by the following model (Warner et al. 1979; Li & Loken 2002):

\[ \begin{aligned} y_{ij} &= \mu + e_{ij} \\ e_{ij} &= a_{i} + b_{j} + \epsilon_{ij} \\ \{ (a_{1}, b_{1}), \ldots, (a_{n}, b_{n}) \} &\sim N(0,\Sigma_{ab}) \\ \{ (\epsilon_{ij}, \epsilon_{ji}) : \; i \neq j\} &\sim N(0,\Sigma_{\epsilon}), \text{ where } \\ \Sigma_{ab} = \begin{pmatrix} \sigma_{a}^{2} & \sigma_{ab} \\ \sigma_{ab} & \sigma_{b}^2 \end{pmatrix} \;\;\;\;\; &\Sigma_{\epsilon} = \sigma_{\epsilon}^{2} \begin{pmatrix} 1 & \rho \\ \rho & 1 \end{pmatrix} \end{aligned} \]

• Capture some interesting features of networks …
• … but what about exogenous explanatory variables?

\[ \begin{aligned} y_{i,j} = \beta_d^T \textbf{x}_{d,i,j} + \beta_r^T \textbf{x}_{r,i} +\beta_c^T \textbf{x}_{c,j} + a_i + b_j + \epsilon_{i,j} \end{aligned} \] Variables we might want to include:

(Hoff 2005; Westveld & Hoff 2010; Hoff et al. 2013; Fosdick & Hoff 2015; Minhas et al. 2016)

Threshold model: linking latent \(Z\) to \(Y\)

• \(y_{ij} = 1(z_{ij}>0)\)
• \(z_{ij} = \beta^{T} x_{ij} + e_{ij}\)

Social relations model: inducing network covariance

• \(e_{ij} = a_{i} + b_{j} + \epsilon_{ij}\)
• \(\{(a_{1},b_{1}),\ldots,(a_{n},b_{n})\} \sim N(0, \Sigma_{ab})\)
• \(\{(\epsilon_{ij},\epsilon_{ji}) i \neq j \} \sim N(0, \Sigma_{\epsilon})\)

Gibbs Sampler for Bayesian estimation

An MCMC routine providing a fit to an additive and multiplicative effects (AME) regression model to relational data of various type

Arguments:

Nodal covariates should be structured as:

• an \(n \times p\) matrix of covariates, where \(n\) corresponds to number of actors and \(p\) covariates
• In the directed case, row and nodal covariates need to be inputted separately into Xrow and Xcol

Xn[1:10,]

##          pop      gdp polity
## ARG 3.548755 5.864710   7.18
## AUL 2.895912 6.011414  10.00
## BEL 2.314514 5.370685  10.00
## BNG 4.789989 5.177956   5.00
## BRA 5.070915 6.963597   8.00
## CAN 3.377588 6.531009  10.00
## CHN 7.091101 8.114522  -7.00
## COL 3.652734 5.324862   7.82
## EGY 4.063542 5.371521  -3.55
## FRN 4.082272 7.101956   9.00

Dyadic covariates should be structured as:

• an \(n \times n \times p\) array of covariates, where \(p\) now corresponds to the number of dyadic covariates

Xd[1:3,1:3,]

conflicts

##     ARG AUL BEL
## ARG  NA   0   0
## AUL   0  NA   0
## BEL   0   0  NA

distance

##       ARG   AUL   BEL
## ARG    NA 11.72 11.31
## AUL 11.72    NA 16.71
## BEL 11.31 16.71    NA

shared_igos

##      ARG  AUL  BEL
## ARG   NA 3.83 3.92
## AUL 3.83   NA 4.02
## BEL 3.92 4.02   NA

fitSRM = ame(Y=Y,
             Xdyad=Xd, # incorp dyadic covariates
             Xrow=Xn, # incorp sender covariates
             Xcol=Xcol, # incorp receiver covariates
             symmetric=FALSE, # tell AME trade is directed
             intercept=TRUE, # add an intercept             
             model='nrm', # model type
             rvar=TRUE, # sender random effects (a)
             cvar=TRUE, # receiver random effects (b)
             dcor=TRUE, # dyadic correlation
             R=0, # we'll get to this later
             nscan=10000, burn=5000, odens=25,
             plot=FALSE, print=FALSE, gof=TRUE
             )

objects returned in fitSRM

names(fitSRM)

##  [1] "BETA" "VC"   "APM"  "BPM"  "U"    "V"    "UVPM" "EZ"   "YPM"  "GOF"

paramPlot(fitSRM$BETA)

grid.arrange( paramPlot(fitSRM$VC),
  arrangeGrob( abPlot(fitSRM$APM, 'Sender Effects'),
               abPlot(fitSRM$BPM, 'Receiver Effects') ), ncol=2 )

gofPlot(fitSRM$GOF, symmetric=FALSE)

• Homophily: "birds of a feather flock together"
• Stochastic equivalence: nothing as pithy to say here, but this model focuses on community detection

Lets build on what we have so far and find an expression for \(\gamma\):

\[ y_{ij} \approx \beta^{T} X_{ij} + a_{i} + b_{j} + \gamma(u_{i},v_{j}) \]

(Holland et al. 1983; Nowicki & Snijders 2001; Rohe et al. 2011; Airoldi et al. 2013)

Each node \(i\) is a member of an (unknown) latent class:

\[ \textbf{u}_{i} \in \{1, \ldots, K \}, \; i \in \{1,\ldots, n\} \\ \] The probability of a tie between \(i\) and \(j\) is:

\[ Pr(Y_{ij}=1 | \textbf{u}_{i}, \textbf{u}_{j}) = \theta_{\textbf{u}_{i} \textbf{u}_{j}} \]

• Nodes in the network may have a small or high probability of ties: \(\theta_{kk}\) may be small or large
• Nodes in the same class are stochastically equivalent

Software packages:

• CRAN: statnet (Handcock et al. 2016)
• CRAN: blockmodels (Leger 2015)

(Hoff et al. 2002; Krivitsky et al. 2009; Sewell & Chen 2015)

Each node \(i\) has an unknown latent position

\[ \textbf{u}_{i} \in \mathbb{R}^{k} \]

The probability of a tie from \(i\) to \(j\) depends on the distance between them

\[ Pr(Y_{ij}=1 | \textbf{u}_{i}, \textbf{u}_{j}) = \theta - |\textbf{u}_{i} - \textbf{u}_{j}| \]

• Nodes nearby one another are more likely to have a tie, and will likely have similar ties to others

Software packages:

• CRAN: latentnet (Krivitsky et al. 2015)
• CRAN: VBLPCM (Salter-Townshend 2015)

(Hoff 2003; Hoff 2007)

Each node \(i\) has an unknown latent factor

\[ \textbf{u}_{i} \in \mathbb{R}^{k} \]

The probability of a tie from \(i\) to \(j\) depends on their latent factors

\[ \begin{aligned} Pr(Y_{ij}=1 | \textbf{u}_{i}, \textbf{u}_{j}) =& \theta + \textbf{u}_{i}^{T} \Lambda \textbf{u}_{j} \, \text{, where} \\ &\Lambda \text{ is a } K \times K \text{ diagonal matrix} \end{aligned} \]

• Can account for both stochastic equivalence and homophily
• Comes at the cost of harder to interpret multiplicative factors … lets see what I mean

Software packages:

• CRAN: amen (Hoff et al. 2015)

Multiplicative effects can be added by toggling the R input parameter

fitAME = ame(Y=Y,
             Xdyad=Xd, # incorp dyadic covariates
             Xrow=Xn, # incorp sender covariates
             Xcol=Xcol, # incorp receiver covariates
             symmetric=FALSE, # tell AME trade is directed
             intercept=TRUE, # add an intercept             
             model='nrm', # model type
             rvar=TRUE, # sender random effects (a)
             cvar=TRUE, # receiver random effects (b)
             dcor=TRUE, # dyadic correlation
             R=2, # 2 dimensional multiplicative effects
             nscan=10000, burn=25, odens=25,
             plot=FALSE, print=FALSE, gof=TRUE
             )

gofPlot(fitAME$GOF, symmetric=FALSE)

ggCirc(Y=Y, U=fitAME$U, V=fitAME$V)

• At its core, AME is just a GLM with random effects used to ensure that we can treat dyadic observations as conditionally independent
• AME can be used:
  • on both undirected and directed data,
  • on longitudinal and static networks,
  • and on a variety of distribution types we commonly encounter in political science (binomial, gaussian, and ordinal).

Cranmer et al. (2017)

• Great paper comparing a few inferential network approaches
• Utilized Swiss climate change policy collaboration network as application (Ingold, 2008)

Out-of-sample Network Cross-Validation

Does AME actually reduce bias?

• Cranmer & Desmarias (2017)

Hoff provides an argument that rests on exchangeability (Aldous, 1985)

Basis of simulation analysis

# Network simulation
simY = simulate.formula(network(n) ~ edges + edgecov(edgeVar) + networkTerm, 
                 coef=c(
                   interceptValue,
                   dyadParamValue,
                   netParamValue
                   ) )

# Run ergm
ergm(simY ~ edges + edgecov(edgeVar) + networkTerm)

# Run ame with and without multiplicative effects
ame(simY, Xdyad=edges, K=0)
ame(simY, Xdyad=edges, K=2)

Other things

Have been working with Hoff to:

• handle networks with changing actor compositions
• handle missing data
• transitioning package to C++
• lots of other UI related changes…

Lots of cool stuff been/being done with this general framework:

• LFM is not the end all be all model [duh], it's a powerful framework that has proven useful for some

• A lot of other things going on:
  • Community structure in longitudinal, multidimensional arrays (Mucha et al. 2010)
  • Multilinear tensor regression (Hoff 2015, Schein et al. 2015, Minhas et al. 2016)
  • Intersection of network based methods to text analysis (Henry et al. 2016, Huang et al. 2015)
• Takeaway here is that these methods are useful when we study systems in which interactions are interdependent

• These interdependent relations may at times be of interest themselves or in other cases may just help us to better predict